1.1. Downloading EMBOSS

1.1.1. Downloading with a Web Browser

This will always be a link to the most recent version of EMBOSS. In the example given it is a link to EMBOSS-6.0.1.tar.gz. The other gz files are the EMBOSS-associated EMBASSY packages. These are extra files you can apply to the base EMBOSS installation. The EMBASSY packages are dealt with in a separate section of this book: you can download these optional files at the same time as EMBOSS-latest.tar.gz if you intend installing them.

1.1.2. Downloading by Anonymous FTP

1.1.2.1. Interactive FTP

Change directory to the location in which you wish to download the source code. In this example you will download the source to /usr/local/src/EMBOSS. Then start your FTP client and point it to emboss.open-bio.org.

Enter your email address here as the password for user anonymous. You could, in fact, type anything but it is a common courtesy to use your email address so the developers can get some idea of which sites have downloaded the software. Your email address will only be used for gathering such statistics. The FTP server will respond with something similar to the following:

You should now set your FTP client to use passive mode. How to do so depends on your FTP client. It is usually done by using the command passive or the command pasv; sometimes the FTP client has no such command and will usually already be in passive mode. To find out which, if any, command to type you can use the help command to show which commands your FTP client supports.

The file EMBOSS-latest.tar.gz is a link on the FTP server which points to the latest version of the EMBOSS source code. The directory listing from the ls command shows that, in this example, it points to EMBOSS-6.0.1.tar,gz. So, what you've really downloaded is the EMBOSS 6.0.1 source code. The remaining gz files shown in the directory listing are the EMBASSY packages; these are EMBOSS-associated packages which you can optionally install once EMBOSS itself has been installed. If you intend installing the EMBASSY packages then now is a good time to get them too.

If you wish, you can download all the gz files using a single command as long as you set the server to turn prompting off. To do this use the prompt command

ftp>prompt
Interactive mode off
ftp>

If, instead, the server responded with Interactive mode on, then the server already had prompting turned off; in that case type prompt again.

You can now download all the gz files using mget *gz. Note, however, that this will download both EMBOSS-latest.tar.gz and EMBOSS-6.0.1.tar.gz so there will be some unnecessary bandwidth used.

1.1.2.2. FTP using wget

The program wget can be used to download a remote directory non-interactively. More details on wget can be obtained from the Free Software Foundation (http://www.gnu.org). Assuming you have wget installed, use the following command; it will generate a lot of output on the screen:

This command will have created a directory called emboss.open-bio.org/pub/EMBOSS and downloaded the gz files into that directory. Experienced UNIX users may take the opportunity to make a symbolic link called EMBOSS to this directory although it is not, of course, essential.

1.1.3. Unpacking the Source Code

You will have downloaded the EMBOSS source code to a suitable directory. Move to whichever directory you chose (e.g. cd /usr/local/src/emboss) and list the directory to make sure. We'll ignore the EMBASSY packages for now; they are described elsewhere in this book and, besides, you need to install EMBOSS before installing any EMBASSY package.

%ls
EMBOSS-latest.tar.gz

The EMBOSS-latest.tar.gz file is a compressed binary file and requires that your UNIX distribution has the gunzip program installed. Check that the command:

which gunzip

gives a positive response. If not then install the gzip package from whichever freeware site your UNIX distribution uses or, alternatively, compile the source code from the gzip homepage (http://www.gzip.org) which contains compilation instructions.

You unpack the EMBOSS distribution by typing:

gunzip EMBOSS-latest.tar.gz

This will create a file called EMBOSS-latest.tar. Such tar files are archive files containing the individual source code files.

You must now extract the archive using the tar program:

tar xf EMBOSS-latest.tar

This will create a new directory, EMBOSS-6.0.1: the exact name will depend on the version of EMBOSS being unpacked. Enter the directory and type ls to show the files. The directory listing should look something like this: